Version 2.22.2
Genome Detective Platform

NGS Details (SRR3458562_Metagenome_example): Rotavirus A (segment 8)

Assembly

1059 (1 contig(s))
2133.2
20728
1337.46 rpm (after QC)
0
de novo + reference guided assembly
Bcf Tools

Coverage Map

Variant Tables

Assignment

Rotavirus A (Taxonomy ID: 28875)
80.2644
86.1635
1
1

Alignment

segment 8
1282.0 (NT) + 1912.0 (AA) = 3194.0
74.6785
Global, seeded, nucleotide + amino acids (AGA)

Alignment Detailed Statistics

BeginEndCoverageScoreConcordanceMatchesIdentitiesI/D/M/F*Stop Codons
NT11059100%128260.5%1059 (100%)850 (80.3%)0/0
Mutations:
70C>T 88T>C 99A>G 103T>C 109T>A 115T>C 117A>G 127T>A 131G>T 132C>G 137C>T 145T>A 151A>G 160G>A 163C>T 164A>C 165T>A 166G>A 172G>A 179G>A 187T>A 196A>T 199A>T 205G>A 208T>G 211T>A 217T>C 220G>A 226G>T 232T>C 235T>G 241T>C 253C>A 261T>A 268A>T 269A>C 270T>C 271T>A 279C>A 283G>A 289T>G 290A>G 295G>A 298A>T 307T>G 308C>T 310A>G 317T>A 319G>T 325G>T 328G>T 332G>T 334A>T 335A>G 337C>T 340C>T 341T>G 343T>G 345A>G 350T>C 352A>T 356C>A 357G>A 364A>T 367A>T 368A>G 373G>A 377T>C 382A>G 391G>A 392A>C 393T>G 394A>G 395C>A 397T>A 399A>G 403A>G 408C>A 409A>T 415T>C 416A>G 418T>G 421A>T 424T>C 436T>G 439A>G 440C>T 442T>G 452A>G 453C>T 457G>A 460T>A 469A>T 472G>C 475T>A 490T>G 493A>T 494A>G 495T>C 496A>C 502A>T 511A>G 515A>G 517T>A 520A>T 529C>T 532T>A 535C>T 538C>T 541C>A 551C>T 553A>G 556T>A 559T>C 560T>C 562A>G 565A>G 569C>A 570A>G 571A>C 572T>C 574G>A 584C>T 592G>A 611G>A 613T>A 617T>A 643T>A 644G>T 645T>C 646T>A 659T>C 661A>G 662G>A 664C>T 670A>G 671C>T 673T>G 676A>G 685T>C 691G>A 697T>A 703C>T 715G>A 721T>C 724T>C 728A>G 736G>A 751T>G 757C>T 760T>A 763C>T 769A>T 772T>C 775A>T 791G>A 792T>A 796A>G 798C>A 802A>G 803G>A 804T>A 807A>T 808T>G 810A>T 811T>A 814T>G 820C>T 838T>A 841T>A 847A>G 859A>G 868A>T 880G>A 886T>C 889A>T 895C>A 898G>A 904A>G 906G>A 907G>A 908T>C 910G>A 913T>G 922A>G 928A>G 930C>G 936A>G 937A>T 943A>G 949A>G 952G>A 961G>T 970A>G 976C>T 979A>G 989G>A 991T>A 994C>A 995G>A 1005C>T 1010A>G 1018G>A 1022A>G 1023T>G 1024G>C 1028G>A 1030T>A 1031T>A
CDS
1318100%191288.6%318 (100%)274 (86.2%)0/0/0/01
Protein mutations:
K18R (99A>G) N24S (117A>G) A29C (131G>T 132C>G) M40Q (164A>C 165T>A 166G>A) D45N (179G>A) F72Y (261T>A) I75P (269A>C 270T>C 271T>A) T78N (279C>A) M82V (290A>G) L91I (317T>A 319G>T) A96S (332G>T 334A>T) N97D (335A>G 337C>T) S99A (341T>G 343T>G) N100S (345A>G) R104K (356C>A 357G>A) I108V (368A>G) I116R (392A>C 393T>G 394A>G) K118R (399A>G) P121H (408C>A 409A>T) I124V (416A>G 418T>G) D130E (436T>G) T136V (452A>G 453C>T) Q142H (472G>C) I150A (494A>G 495T>C 496A>C) I157V (515A>G 517T>A) Q175S (569C>A 570A>G 571A>C) V189I (611G>A 613T>A) L191M (617T>A) D199E (643T>A) V200S (644G>T 645T>C 646T>A) V206I (662G>A 664C>T) I228V (728A>G) V249N (791G>A 792T>A) T251N (798C>A) V253N (803G>A 804T>A) N254M (807A>T 808T>G) N255I (810A>T 811T>A) D256E (814T>G) D283E (895C>A) R287K (906G>A 907G>A) P295R (930C>G) K297S (936A>G 937A>T) V315I (989G>A 991T>A) V317I (995G>A)
Codon mutations:
TGC8TGT (70C>T) AAT14AAC (88T>C) AAA18AGA (99A>G) TTT19TTC (103T>C) CCT21CCA (109T>A) AAT23AAC (115T>C) AAT24AGT (117A>G) ATT27ATA (127T>A) GCT29TGT (131G>T 132C>G) CTG31TTG (137C>T) GCT33GCA (145T>A) GTA35GTG (151A>G) AAG38AAA (160G>A) GAC39GAT (163C>T) ATG40CAA (164A>C 165T>A 166G>A) AAG42AAA (172G>A) GAT45AAT (179G>A) ATT47ATA (187T>A) GGA50GGT (196A>T) ATA51ATT (199A>T) CCG53CCA (205G>A) CCT54CCG (208T>G) CCT55CCA (211T>A) TTT57TTC (217T>C) AAG58AAA (220G>A) CGG60CGT (226G>T) AAT62AAC (232T>C) ACT63ACG (235T>G) GAT65GAC (241T>C) GGC69GGA (253C>A) TTT72TAT (261T>A) ACA74ACT (268A>T) ATT75CCA (269A>C 270T>C 271T>A) ACT78AAT (279C>A) AAG79AAA (283G>A) GCT81GCG (289T>G) ATG82GTG (290A>G) TTG83TTA (295G>A) ATA84ATT (298A>T) GCT87GCG (307T>G) CTA88TTG (308C>T 310A>G) TTG91ATT (317T>A 319G>T) GTG93GTT (325G>T) ACG94ACT (328G>T) GCA96TCT (332G>T 334A>T) AAC97GAT (335A>G 337C>T) GTC98GTT (340C>T) TCT99GCG (341T>G 343T>G) AAT100AGT (345A>G) TTA102CTT (350T>C 352A>T) CGA104AAA (356C>A 357G>A) GTA106GTT (364A>T) TCA107TCT (367A>T) ATA108GTA (368A>G) AGG109AGA (373G>A) TTA111CTA (377T>C) GAA112GAG (382A>G) GTG115GTA (391G>A) ATA116CGG (392A>C 393T>G 394A>G) CGT117AGA (395C>A 397T>A) AAA118AGA (399A>G) GAA119GAG (403A>G) CCA121CAT (408C>A 409A>T) GAT123GAC (415T>C) ATT124GTG (416A>G 418T>G) CTA125CTT (421A>T) TTT126TTC (424T>C) GAT130GAG (436T>G) TTA131TTG (439A>G) CTT132TTG (440C>T 442T>G) ACA136GTA (452A>G 453C>T) CTG137CTA (457G>A) ATT138ATA (460T>A) GGA141GGT (469A>T) CAG142CAC (472G>C) TCT143TCA (475T>A) ACT148ACG (490T>G) ACA149ACT (493A>T) ATA150GCC (494A>G 495T>C 496A>C) GCA152GCT (502A>T) GGA155GGG (511A>G) ATT157GTA (515A>G 517T>A) GTA158GTT (520A>T) AAC161AAT (529C>T) GCT162GCA (532T>A) GCC163GCT (535C>T) TTC164TTT (538C>T) ACC165ACA (541C>A) CTA169TTG (551C>T 553A>G) ACT170ACA (556T>A) TAT171TAC (559T>C) TTA172CTG (560T>C 562A>G) GAA173GAG (565A>G) CAA175AGC (569C>A 570A>G 571A>C) TTG176CTA (572T>C 574G>A) CTG180TTG (584C>T) CAG182CAA (592G>A) GTT189ATA (611G>A 613T>A) TTG191ATG (617T>A) GAT199GAA (643T>A) GTT200TCA (644G>T 645T>C 646T>A) TTA205CTG (659T>C 661A>G) GTC206ATT (662G>A 664C>T) GAA208GAG (670A>G) CTT209TTG (671C>T 673T>G) CGA210CGG (676A>G) TAT213TAC (685T>C) AAG215AAA (691G>A) GCT217GCA (697T>A) ATC219ATT (703C>T) AAG223AAA (715G>A) CAT225CAC (721T>C) TAT226TAC (724T>C) ATT228GTT (728A>G) AAG230AAA (736G>A) GCT235GCG (751T>G) CAC237CAT (757C>T) GCT238GCA (760T>A) GAC239GAT (763C>T) GTA241GTT (769A>T) TAT242TAC (772T>C) GCA243GCT (775A>T) GTT249AAT (791G>A 792T>A) AAA250AAG (796A>G) ACT251AAT (798C>A) GGA252GGG (802A>G) GTT253AAT (803G>A 804T>A) AAT254ATG (807A>T 808T>G) AAT255ATA (810A>T 811T>A) GAT256GAG (814T>G) AAC258AAT (820C>T) ATT264ATA (838T>A) ATT265ATA (841T>A) CAA267CAG (847A>G) GCA271GCG (859A>G) TCA274TCT (868A>T) CAG278CAA (880G>A) AAT280AAC (886T>C) ACA281ACT (889A>T) GAC283GAA (895C>A) GTG284GTA (898G>A) AAA286AAG (904A>G) AGG287AAA (906G>A 907G>A) TTG288CTA (908T>C 910G>A) CTT289CTG (913T>G) AAA292AAG (922A>G) AAA294AAG (928A>G) CCA295CGA (930C>G) AAA297AGT (936A>G 937A>T) CCA299CCG (943A>G) AAA301AAG (949A>G) GGG302GGA (952G>A) ACG305ACT (961G>T) AAA308AAG (970A>G) GAC310GAT (976C>T) GAA311GAG (979A>G) GTT315ATA (989G>A 991T>A) GGC316GGA (994C>A) GTT317ATT (995G>A)
Proteins
1318100%191288.6%318 (100%)274 (86.2%)0/0/0/01
Protein mutations:
K18R (99A>G) N24S (117A>G) A29C (131G>T 132C>G) M40Q (164A>C 165T>A 166G>A) D45N (179G>A) F72Y (261T>A) I75P (269A>C 270T>C 271T>A) T78N (279C>A) M82V (290A>G) L91I (317T>A 319G>T) A96S (332G>T 334A>T) N97D (335A>G 337C>T) S99A (341T>G 343T>G) N100S (345A>G) R104K (356C>A 357G>A) I108V (368A>G) I116R (392A>C 393T>G 394A>G) K118R (399A>G) P121H (408C>A 409A>T) I124V (416A>G 418T>G) D130E (436T>G) T136V (452A>G 453C>T) Q142H (472G>C) I150A (494A>G 495T>C 496A>C) I157V (515A>G 517T>A) Q175S (569C>A 570A>G 571A>C) V189I (611G>A 613T>A) L191M (617T>A) D199E (643T>A) V200S (644G>T 645T>C 646T>A) V206I (662G>A 664C>T) I228V (728A>G) V249N (791G>A 792T>A) T251N (798C>A) V253N (803G>A 804T>A) N254M (807A>T 808T>G) N255I (810A>T 811T>A) D256E (814T>G) D283E (895C>A) R287K (906G>A 907G>A) P295R (930C>G) K297S (936A>G 937A>T) V315I (989G>A 991T>A) V317I (995G>A)
Codon mutations:
TGC8TGT (70C>T) AAT14AAC (88T>C) AAA18AGA (99A>G) TTT19TTC (103T>C) CCT21CCA (109T>A) AAT23AAC (115T>C) AAT24AGT (117A>G) ATT27ATA (127T>A) GCT29TGT (131G>T 132C>G) CTG31TTG (137C>T) GCT33GCA (145T>A) GTA35GTG (151A>G) AAG38AAA (160G>A) GAC39GAT (163C>T) ATG40CAA (164A>C 165T>A 166G>A) AAG42AAA (172G>A) GAT45AAT (179G>A) ATT47ATA (187T>A) GGA50GGT (196A>T) ATA51ATT (199A>T) CCG53CCA (205G>A) CCT54CCG (208T>G) CCT55CCA (211T>A) TTT57TTC (217T>C) AAG58AAA (220G>A) CGG60CGT (226G>T) AAT62AAC (232T>C) ACT63ACG (235T>G) GAT65GAC (241T>C) GGC69GGA (253C>A) TTT72TAT (261T>A) ACA74ACT (268A>T) ATT75CCA (269A>C 270T>C 271T>A) ACT78AAT (279C>A) AAG79AAA (283G>A) GCT81GCG (289T>G) ATG82GTG (290A>G) TTG83TTA (295G>A) ATA84ATT (298A>T) GCT87GCG (307T>G) CTA88TTG (308C>T 310A>G) TTG91ATT (317T>A 319G>T) GTG93GTT (325G>T) ACG94ACT (328G>T) GCA96TCT (332G>T 334A>T) AAC97GAT (335A>G 337C>T) GTC98GTT (340C>T) TCT99GCG (341T>G 343T>G) AAT100AGT (345A>G) TTA102CTT (350T>C 352A>T) CGA104AAA (356C>A 357G>A) GTA106GTT (364A>T) TCA107TCT (367A>T) ATA108GTA (368A>G) AGG109AGA (373G>A) TTA111CTA (377T>C) GAA112GAG (382A>G) GTG115GTA (391G>A) ATA116CGG (392A>C 393T>G 394A>G) CGT117AGA (395C>A 397T>A) AAA118AGA (399A>G) GAA119GAG (403A>G) CCA121CAT (408C>A 409A>T) GAT123GAC (415T>C) ATT124GTG (416A>G 418T>G) CTA125CTT (421A>T) TTT126TTC (424T>C) GAT130GAG (436T>G) TTA131TTG (439A>G) CTT132TTG (440C>T 442T>G) ACA136GTA (452A>G 453C>T) CTG137CTA (457G>A) ATT138ATA (460T>A) GGA141GGT (469A>T) CAG142CAC (472G>C) TCT143TCA (475T>A) ACT148ACG (490T>G) ACA149ACT (493A>T) ATA150GCC (494A>G 495T>C 496A>C) GCA152GCT (502A>T) GGA155GGG (511A>G) ATT157GTA (515A>G 517T>A) GTA158GTT (520A>T) AAC161AAT (529C>T) GCT162GCA (532T>A) GCC163GCT (535C>T) TTC164TTT (538C>T) ACC165ACA (541C>A) CTA169TTG (551C>T 553A>G) ACT170ACA (556T>A) TAT171TAC (559T>C) TTA172CTG (560T>C 562A>G) GAA173GAG (565A>G) CAA175AGC (569C>A 570A>G 571A>C) TTG176CTA (572T>C 574G>A) CTG180TTG (584C>T) CAG182CAA (592G>A) GTT189ATA (611G>A 613T>A) TTG191ATG (617T>A) GAT199GAA (643T>A) GTT200TCA (644G>T 645T>C 646T>A) TTA205CTG (659T>C 661A>G) GTC206ATT (662G>A 664C>T) GAA208GAG (670A>G) CTT209TTG (671C>T 673T>G) CGA210CGG (676A>G) TAT213TAC (685T>C) AAG215AAA (691G>A) GCT217GCA (697T>A) ATC219ATT (703C>T) AAG223AAA (715G>A) CAT225CAC (721T>C) TAT226TAC (724T>C) ATT228GTT (728A>G) AAG230AAA (736G>A) GCT235GCG (751T>G) CAC237CAT (757C>T) GCT238GCA (760T>A) GAC239GAT (763C>T) GTA241GTT (769A>T) TAT242TAC (772T>C) GCA243GCT (775A>T) GTT249AAT (791G>A 792T>A) AAA250AAG (796A>G) ACT251AAT (798C>A) GGA252GGG (802A>G) GTT253AAT (803G>A 804T>A) AAT254ATG (807A>T 808T>G) AAT255ATA (810A>T 811T>A) GAT256GAG (814T>G) AAC258AAT (820C>T) ATT264ATA (838T>A) ATT265ATA (841T>A) CAA267CAG (847A>G) GCA271GCG (859A>G) TCA274TCT (868A>T) CAG278CAA (880G>A) AAT280AAC (886T>C) ACA281ACT (889A>T) GAC283GAA (895C>A) GTG284GTA (898G>A) AAA286AAG (904A>G) AGG287AAA (906G>A 907G>A) TTG288CTA (908T>C 910G>A) CTT289CTG (913T>G) AAA292AAG (922A>G) AAA294AAG (928A>G) CCA295CGA (930C>G) AAA297AGT (936A>G 937A>T) CCA299CCG (943A>G) AAA301AAG (949A>G) GGG302GGA (952G>A) ACG305ACT (961G>T) AAA308AAG (970A>G) GAC310GAT (976C>T) GAA311GAG (979A>G) GTT315ATA (989G>A 991T>A) GGC316GGA (994C>A) GTT317ATT (995G>A)
*: Inserts / Deletes / Misaligned / Frameshifts

Analysis details

This analysis was performed with panviral2.43